title: Next-generation sequencing facilitates quantitative analysis of miRNAs of cetuximab-resistant colorectal cancer (HCT116-R) cells

city: Hefei

first: Wulin

last: Shan

state: Anhui

address: Huanhudong Road 107

institute: The First Affiliated Hospital of University of Science and Technology of China

summary: Total RNAs were isolated from three groups, including A group (0×10^9/mL PA-MSHA-treated HCT116 cells), B group (0.3×10^9/mL PA-MSHA-treated HCT116 cells) and C group (0.4×10^9/mL PA-MSHA-treated HCT116 cells). MiRNA sequencing was performed to assess differential expression using next-generation sequencing. The data showed that most miRNAs levels were different in A, B and C groups. Importantly, miR-7-5p was greatly increased in a dose-dependent manner.

overall_design: MiRNA sequencing was performed to assess differential expression of miRNAs in A, B and C groups using next-generation sequencing.

first: Huanhuan

last: Zhang


title: Transcriptome sequencing of adventitious root development in four stages of Pyrus ussuriensis Maxim

status: Public on Aug 13 2021

city: Qingdao

first: Wencheng

last: Wang

state: Shandong province

address: 700,Changcheng Road, Chengyang District

department: College of Horticulture

country: China

institute: Qingdao Agricultural University

type: Expression profiling by high throughput sequencing

summary:
Purpose: The goals of this study was to obtain transcriptome data from five developmental stages of adventitious roots of Pyrus ussuriensis Maxim using transcriptome analysis (RNA-Seq) and qRT-PCR analysis.

Mathods: The mRNA profiles of the adventitious root development of Pyrus ussuriensis on day 0, day 3, day 6, day 9, and day 12 were examined by deep sequencing, in triplicate, using Illumina HiSeq 2000. Ultra™ RNA LibraryPrep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and indexcodes were added to attribute sequences to each sample. qRT–PCR validation was performed using TaqMan and SYBR Green assays.

Results: The transcriptome regulation analysis of the Pyrus ussuriensis adventitious root formation was performed on this study. And a total of 19,470 DEGs (Differentially Expressed Gene), which were mainly enriched in hormone synthesis and signaling pathways, energy metabolism, synthesis and metabolism of secondary products, were detected. the key regulatory genes of adventitious root formation were screened, mainly including the gene family WOX, LBD and SRS. Auxin, plays a key role in the induction and development of root primordium, its signal transduction pathway-related genes were up-regulated during the induction period of root primordium, and down-regulated during the development of root primordia. Carotenoids is the precursor substance of abscisic acid synthetize. And for the reasons that the genes of carotenoid synthesis and signal transduction pathway of abscisic acid were down-regulated during the period of stable development and the root primordium induction, and up-regulated during the period of root primordium development of adventitious root, it was supposed that abscisic acid was a control substance, that regulated the metabolic network of development of adventitious roots.

Conclusions: Our results provide a comprehensive high-resolution characterization of gene expression profiles during the pear root transition process.A number of DEGs were detected from the root primordium to adventitious root  growth stages, and these belonged to hormone metabolism pathways.These results provide a valuable resource for studies in other closely related species with similar agricultural and productive value. The differentially expressed genes dataset will also provide useful candidate genes for functional analysis of pear rooting.

overall_design: Using the Pyrus bretschneideri genome as a reference sequence, the mRNA profiles of the adventitious root development of Pyrus ussuriensis on day 0, day 3, day 6, day 9, and day 12 were examined by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Dingli

last: Li


title: Expansion of FCGR3A+ macrophages, FCN1+ mo-DC, and plasmacytoid dendritic cells associated with severe skin disease in systemic sclerosis

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

country: USA

institute: University of Pittsburgh

summary: We sought a comprehensive understanding of myeloid cell types driving fibrosis in diffuse  cutaneous systemic sclerosis (dcSSc) skin.  T-stochastic neighbor embedding analysis of single cell transcriptome data revealed 12  myeloid cell clusters, nine of which paralleled previously described HC Mφ/DC clusters and three of  which were dcSSc-specific myeloid cell clusters. One SSc-associated macrophage cluster, highly  expressing FCGR3A, on pseudotime analysis was suggested to derive from normal CCR1+ and MARCO+ macrophages. A second SSc-associated myeloid population, highly expressed monocyte  markers: FCN1, EREG, S100A8 and S100A9, but was closely related to cDC2 on pseudotime  analysis and identified as Mo-DC. Mo-DC were associated with more severe skin disease.  Proliferating macrophages and plasmacytoid dendritic cells were detected almost exclusively in  dcSSc skin, the latter clustering with B cells and apparently derived from lymphoid progenitors.  Transcriptional signatures in these and other myeloid populations indicate innate  immune activation, possibly through TLRs, and highly upregulated chemokines. However, the  appearance and activation of myeloid cells is variable between patients, indicating differing  underlying pathogenesis and/or temporal disease activity.

overall_design: We analyzed the transcriptomes of 2,465 myeloid cells skin biopsies from 10 healthy  controls (HCs) and 12 dcSSc patients by single-cell RNA-sequencing (scRNA-seq). Monocytederived dendritic cells were stained by immunohistochemistry and immunofluorescence targeting  FCN1.

first: Dan

last: Xue

first: Christina

last: Morse

first: Yi

last: Yang

first: Robyn

last: Domsic

first: Dinesh

last: Khanna

first: Robert

last: Lafyatis


title: Application of Array CGH technique for the clinical diagnosis of developmental delay and congenital malformations in Saudi Arabia

city: Jeddah

first: Sajjad

last: Karim

state: Makka

address: Sulemania, CEGMR-80216

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

type: Genome variation profiling by genome tiling array

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptional toxicity of imidazolium- and cholinium-based ionic liquids

city: Aveiro

first: Guilherme

middle: de Abreu

last: Jeremias

address: Campus Universitário de Santiago

department: Biology Department

country: Portugal

institute: University of Aveiro

summary: Ionic Liquids are a broad group of salts with low melting points that can be specifically tuned for a broad range of applications. Despite being initially considered “green” solvents, their better environmental friendliness compared to traditional solvents has been increasingly challenged. In this study, we aimed to investigate the molecular effects of ILs exposure by using RNA-sequencing to study differential gene expression patterns. Thus, we exposed Daphnia magna to 1-ethyl-3-methylimidazolium chloride ([C2mim]Cl), 1-dodecyl chloride-3-methylimidazolium ([C12mim]Cl) and cholinium chloride ([Chol]Cl). Results suggest that the three ILs share several mechanisms of toxicity, including cellular membrane and cytoskeleton damage, oxidative stress, inhibition of antioxidant enzymes, mitochondrial affectation, changes in protein biosynthesis and energy production, DNA damage, and ultimately, programmed cell death and disease initiation. Overall, the dataset revealed that [C2mim]Cl and [C12mim]Cl were, respectively, the least and the most toxic ILs at the transcriptional level. Also, it is reinforced that [Chol]Cl is not devoid of environmental hazardous potential. Unique gene expression signatures could also be identified for each IL.

overall_design: 12 samples of whole-body mRNA profiles of 48-hours old Daphnia magna: control (3 replicates), exposure to 1-ethyl-3-methylimidazolium chloride (3 replicates), exposure to 1-dodecyl chloride-3-methylimidazolium (3 replicates) and exposure to cholinium chloride (3 replicates)

first: Fátima

last: Jesus

first: Sónia

middle: M

last: Ventura

first: Fernando

last: Gonçalves

first: Jana

last: Asselman

first: Joana

middle: L

last: Pereira


title: Autism risk gene KMT5B deficiency in prefrontal cortex induces synaptic dysfunction and social deficits via alterations of DNA repair and gene transcription

status: Public on Aug 12 2021

city: Buffalo

first: Zhen

last: Yan

state: NY

address: 955 Main St

institute: SUNY Buffalo

summary: We performed RNAseq experiments to examine genome-wide transcriptional changes in PFC of shRNA-Kmt5b KD mice compared to GFP injected control mice.

overall_design: mRNA via RNAseq analysis of three 6-8 week old  shRNA-Kmt5b-injected KD mice  (C57BL/6 x C3H) , and two 6-8 week old GFP-injected control mice (C57BL/6 x C3H) PFC tissue were compared.

first: Jamal

last: Williams


title: MicroRNA expression profiling in a mouse spinal cord injury model [P90, 7d]

city: Norwich

first: Darrell

last: Green

address: Earlham Road

department: Norwich Medical School

country: United Kingdom

institute: University of East Anglia

type: Non-coding RNA profiling by high throughput sequencing

summary: Spinal cord injury (SCI) is a devastating condition resulting in permanent and irreversible deficits. Despite regeneration attempts, the neurons fail due to several dysfunctions. A number of studies have already revealed that, following SCI, microRNAs show two opposite kinds of alterations, one detrimental and one protective. However, there is still little evidence of specific microRNAs involved in axon regrowth. The aim of this project is the characterization of microRNA expression changes in sensorimotor cortex and corticospinal motor neurons, whose axons are severed by SCI.

overall_design: miRNA profiling in SCI mouse model (P90) at a specific time point (7 days). Complete transection of the spinal cord was induced at the C5-C6 level in adult mice (3 WT vs. 3 SCI per each group). At 7 days post injury, the sensorimotor cortex was dissected, collected for RNA extraction and the HD sRNA library was sequenced.

first: Matilde

last: Ghibaudi

first: Marina

last: Boido

first: Irina

last: Mohorianu

first: Elena

last: Signorino

first: Daniela

last: Rovito

first: Diego

last: Garbossa

first: Tamas

last: Dalmay

first: Alessandro

last: Vercelli


title: RIPK1 kinase-dependent gene expression in human astrocytes in vitro

city: Framingham

first: Dimitry

last: Ofengeim

address: 49 New York Avenue

institute: Sanofi

summary: To determine the role of RIPK1 kinase-dependent transcriptional signaling in human fetal-derived astrocytes, we stimulated cells with the RIPK1 kinase-activating stimulus TNF/Smac/zVAD in the presence or absence of the RIPK1 kinase inhibitor Nec-1s. We identified various genes modulated in a RIPK1 kinase-dependent manner in human astrocytes, and the main biological pathways were related to an interferon signaling and anti-viral response.

overall_design: 3 biological replicates of human astrocytes were treated with (1) DMSO, (2) Nec-1s, (3) TNF/Smac/zVAD or (4) TNF/Smac/zVAD/Nec-1s.

first: Matija

last: Zelic

first: Cheng

last: Zhu

first: Tai-he

last: Xia


title: scRNA-seq of E18.5 small intestinal innate lymphoid cells

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

summary: Embryonic innate lymphoid cells (ILCs) were isolated from small intestinal lamina propria to study their transcriptomic profile in the developing tissue.

overall_design: ILCs were isolated from E18.5 small instestines of Rorc(gt)GFP/wt, Rorc(gt)GFP/GFP and Rorc(gt)GFP/GFP x Tbx21-/- (Hashtagged) and FACS-sorted as viable Lineage(CD19, CD3, CD5, F4/80,FceRIa, Gr-1)-CD45+CD122+ and/or CD127+ combined with the following 25 CITE-Seq antibodies: CD49b, NK1.1, DNAM1, CD3, CCR6, NKp46, CD117, Nrp-1, NKG2D, TCRgd, TCRb, CD49a, CXCR5,CD27, CD200R1, CD4, PD-1, CD127 PE + anti PE, a4b7 + anti-Biotin, ICOS, Sca-1, ST2, CD25, KLRG1

first: Christina

last: Stehle

first: Timo

last: Rückert

first: Rémi

last: Fiancette

first: Dominika

middle: W

last: Gajdasik

first: Claire

last: Willis

first: Carolin

last: Ulbricht

first: Mir-Farzin

last: Mashreghi

last: Finke

first: Anja

middle: E

last: Hauser

first: David

middle: R

last: Withers

first: Hyun-Dong

last: Chang

first: Jakob

last: Zimmermann

first: Chiara

last: Romagnani


title: bulk RNA-seq of adult (4 w) small intestinal innate lymphoid cells

summary: Innate lymphoid cells (ILCs) were isolated from small intestinal lamina propria to study their transcriptomic profile in the tissue of adult animals (4 weeks).

overall_design: ILCs were isolated from small instestinal lamina propria of Rorc(gt)GFP/wt, Rorc(gt)GFP/GFP and Rorc(gt)GFP/GFP x Tbx21-/- mice and FACS-sorted as viable Lineage (CD19, CD11c, CD11b, F4/80,FceRIa, Gr-1)-CD45+CD3-RORgt-GFP+  expressing either NKp46 or CD4.

first: Daniela


title: tRNA analysis and two-photon imaging of a 5,000-year-old human femur

first: Darrell

last: Green

summary: We report the application of tRNA profiling in an ancient sample, demonstrating the use of RNA in archeogenomics.

overall_design: Small RNA sequencing of 5,000-year-old bone tissue.

first: Irina

last: Mohorianu


title: Self-renewing islet TCF1+ CD8 T cells undergo interleukin-27 controlled differentiation to become TCF1- terminal effectors during the progression of type 1 diabetes

city: MILWAUKEE

first: Yi-Guang

last: Chen

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin


title: Optimal pooled single-cell RNA-sequencing elucidates gene by environment interactions in circulating immune cells

city: San Francisco

first: Yang

last: Sun

state: CA

address: 513 Parnassus Ave

department: Rheumatology

institute: UCSF

summary: Decoding the genetic architecture of gene expression remains one of the most important problems in human genetics. Because cellular context is often reflective of environmental exposure, mapping context-specific quantitative trait loci (QTLs) and identifying the cellular contexts that modify their effects is critical for understanding the mechanisms by which gene by environment interactions confer disease risk. Here, we introduce a compressed pooling framework for performing genetically multiplexed arrayed single-cell sequencing experiments without the need for prior genotyping. To this end, we developed freemuxlet, an extension of demuxlet, that enables genotype-free demultiplexing of pooled single-cell data applicable to multiplexed single cell RNA- and CITE-seq data. In total, we performed multiplexed CITE-seq across 384 samples from 64 donors over 12 pools in a single day. These results allowed us to generate a map of cell-type specific gene regulatory networks in response to each stimulus. Finally, by integrating imputed genotypes from the individuals, we map genetic variants associated with stimulation in each specific cell type and assess their enrichment for disease associations. Freemuxlet and clue together demonstrate the feasibility of performing population-scale gene-by-environment studies using single-cell RNA-sequencing scalable to between 100 – 1000 individuals.

overall_design: Peripheral blood mononuclear cells (PBMCs) from 64 individuals are incubated with 5 immunomodulatory stimulants and run using a compressed format in 12 reactions of droplet-based single-cell RNA-sequencing to yield transcriptomic and surface proteomic expression.

first: George

middle: C

last: Hartoularos

middle: S

last: Lee

first: Chun

middle: J

last: Ye

first: Anton

last: Ogorodnikov

first: Yichen

last: Si

first: Yun

last: Song

first: Hyun

last: Kang


title: Dysfunctional epidermis increases dermis inflammation in systemic sclerosis: results from a novel epidermal equivalent engineered from SSc keratinocytes.

city: Geneva

first: Barbara

last: Russo

address: Rue Michel Servet 1

department: DEPARTEMENT DE MEDECINE (DEMED)

country: Switzerland

institute: Centre Medical Universitaire

summary: In systemic sclerosis (SSc) evidence suggests abnormal keratinocyte-fibroblast interactions. We investigated the potential epidermal dysfunction in SSc and its effects on dermis homeostasis.   Epidermal equivalents (EE) were generated from six healthy donor (HD) and four SSc keratinocytes. Skin and EE expression of proliferation, differentiation, and activation markers was evaluated by immunohistochemistry. The transcriptomic profile of SSc-EE and HD-EE was identified by RNAseq analysis. EE conditioned medium (CM) was used to stimulate fibroblasts, and their production of interleukin (IL)-6, IL-8, matrix metalloproteinase (MMP)-1, type-I collagen (col-I), and fibronectin was assessed by ELISA.   Compared to HD, SSc-EE exhibited aberrant differentiation, enhanced expression of activation markers, and lower mitotic rate of basal keratinocytes, reproducing most of the abnormalities observed in SSc epidermis. RNAseq analysis revealed that, compared to HD-EE, SSc-EE were characterized by the downregulation of HOX gene family members and by the upregulation of metabolic and oxidative stress molecular pathways. EE-CM enhanced the fibroblast production of IL-6, IL-8, MMP-1, Col-I, and fibronectin (p<0.05). Except for Col-I and fibronectin, this effect was 2-fold higher in the presence of CM generated form SSc-EE. IL-1 was, at least in part, responsible for keratinocyte-dependent fibroblast activation.   SSc-EE recapitulate the in vivo characteristic of SSc epidermis demonstrating that SSc keratinocytes have an intrinsically altered differentiation program possibly due to the downregulation of genes from the HOX family. The increased metabolic and oxidative stress associated with SSc epidermis may participate to dermis chronic inflammation and fibrosis

overall_design: examination of EE from 5 HD and 3 SSc

first: Julia

last: Borowczyk

first: Carlo

last: Chizzolini


title: High resolution chromosome conformation capture from gene promoters at COVID-19, T1D, AS and RBC GWAS loci

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

summary: Genome Wides Association Studies (GWAS) have identified tens of thousands of associations between human genetic variation and common disease. The majority of causative variants lie in regulatory elements that are located some distance from their target genes. High resolution chromosome conformation capture (3C) has proven useful for identifying enhancer-promoter interaction. We employed targeted Capture-C at loci with GWAS for severe COVID-19, Type-1 Diabetes (T1D), Ankylosing spondylitis (AS) and red blood cell traits (RBC)

overall_design: To identify regulatory interactions, we performed high resolution chromatin conformation capture (3C) using NG CaptureC (Davies, NatMethods 2016) or NuTi Capture-C (Downes, NatComms 2020) targeting promoters near variants associated with COVID-19, T1D, AS and RBC. CaptureC was performed in triplicate for Day 10 differentiating erythroid (Ery) cells from three donors, human Embryonic Stem Cells (H1 hESC; WiCell), and Human Umbilical Vein Endothelial Cells (HUVEC; Lonza/Gibco/PromoCell), activated and non-activated CD4+ T-cells, and CD14+ monocytes. Capture was performed with 100-mer biotinylated oligonucleotides targeting sequences adjacent to DpnII sites.

first: Jim

last: Hughes

first: Tony

last: Cutler


title: Cell intrinsic differences in human ALS motor neuron subtypes reveals a common disease mechanism and targeting lipid metabolites

city: Baltimore

first: Hojae

address: 733 north broadway

institute: Johns hopkins medicine

summary: RNA-seq to profile of differential vulnerability between human ocular and spinal motor neurons in ALS

overall_design: Transcriptional profiling of cultured human ocular and spinal motor neurons by RNA-Seq approaches

first: Gabsang


title: MicroRNA expression in a chondroblastic osteosarcoma

first: Darrell

last: Green

summary:
A chondroblastic osteosarcoma was surgically resected.
We performed small RNA sequencing to quantify the microRNAs/ small RNAs expression in the resulting library.

overall_design: The RNA was extracted from the sarcoma. Small RNA sequencing using HD adapters (Xu et al 2015) was performed using Illumina HiSeq 2500.

first: Irina

first: Jeremy

last: Turner

first: Andoni

last: Toms

first: John

last: Nolan

first: Richard

last: Ball

first: Iain

last: McNamara

first: Tamas

last: Dalmay

first: William

last: Fraser


title: Mammalian apoptotic factors regulate bacterial gene expression

city: New York

first: Justin

middle: Shaun Arnold

last: Perry

state: New York

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

summary: Regulated cell death is an integral part of life, having broad impacts on organism development and homeostasis1. Malfunctions within the regulated cell death process, including the clearance of dying cells, can manifest in diverse pathologies throughout various tissues including the gastrointestinal tract2. A long appreciated, yet elusively defined relationship exists between cell death and gastrointestinal pathologies with an underlying microbial component3–6, but the direct impact of dying mammalian cells on bacterial growth is unclear. Here, we advance a concept that several Enterobacteriaceae, including patient derived clinical isolates, have an efficient growth strategy to exploit soluble factors released from dying gut epithelial cells. Mammalian nutrients released after caspase 3/7 dependent apoptosis boosts the growth of multiple Enterobacteriaceae and is observed using primary mouse colonic tissue, murine and human cell lines, multiple apoptotic triggers, and in conventional as well as germ-free mice in vivo. The mammalian cell death nutrients induce a core transcriptional response in pathogenic Salmonella, and we identify the pyruvate formate lyase encoding pflB gene as a key driver of bacterial colonization in three contexts: a foodborne infection model, a TNF and A20 dependent cell death model, and a chemotherapy induced mucositis model. These findings introduce a new layer to the complex host pathogen interaction, where death induced nutrient release (which we term DINNR) acts as a source of fuel for intestinal bacteria, with implications for gut inflammation and cytotoxic chemotherapy treatment.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: The experiment consisted of two conditions: Salmonella grown in live cell supernatants or FADD induced apoptotic supernatants. Each condition consisted of four biological replicates.

first: Christopher

last: Anderson

middle: B

last: Medina

first: Brady

last: Barron

first: Laura

last: Karvelyte

first: Tania

last: Aaes

last: Lambertz

first: Parul

last: Mehrotra

first: Amanda

last: Goncalves

first: Kelly

last: Lemeire

first: Gillian

last: Blancke

first: Vanessa

last: Andries

first: Farzaneh

last: Ghazavi

first: Arne

last: Martens

first: Geert

last: van Loo

first: Lars

last: Vereecke

first: Peter

last: Vandenabeele

first: Kodi

last: Ravichandran


title: Disrupted Macrophage Metabolic Reprogramming in Aged Soleus Muscle During Early Recovery following Disuse Atrophy

city: Salt Lake City

first: Micah

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

summary: Aged skeletal muscle is characterized by impaired muscle recovery following disuse and coincides with an impaired muscle pro-inflammatory macrophage response.  Macrophage inflammatory status (polarization) is regulated by its metabolic state, but to date, little is understood of macrophage metabolism and its relation to macrophage polarization in the context of muscle recovery and aging. Therefore, the purpose of this study was to thoroughly characterize macrophage metabolism and polarization in aged muscle during early recovery from disuse atrophy using single cell RNA sequencing and functional assays. Young (4-5 mo) and old (20-22 mo) male C57BL/6 mice underwent 14 days of hindlimb unloading followed by 4 days of ambulatory recovery.  CD45+ cells were isolated from solei muscles and analyzed using 10x Genomics single cell RNA sequencing.  We found that aged M1 macrophage clusters were characterized with an impaired inflammatory and glycolytic transcriptome and this impairment was accompanied by a suppression of HIF-1α and its immediate downstream target GLUT1.

overall_design: Examination of CD45+ cells from young and old mouse muscle across varying conditions of ambulation, disuse, and recovery.

first: Dennis

middle: K

last: Fix

first: H

middle: A

last: Ekiz

first: Ryan

last: O'Connell


title: Transcriptome study of Sideroxydans lithotrophicus ES-1 grown on different substrates

city: Newark

first: Clara

last: Chan

state: DE

institute: University of Delaware

summary: Compare the gene expression profile of ES-1 grown on Fe(II) and thiosulfate

overall_design: Grow ES-1 on Fe(II)-citrate and thiosulfate and sampled at mid-log, late-log and stationary phase for long-term experiment. Spike in FeCl2 to stationary thiosulfate-grown culture and sampled at 15 min, 35 min and 90 min after the FeCl2 spike. Extract RNA and perform RNA sequencing on those samples.

first: Nanqing

last: Zhou


title: Transcriptomic and metabolic network analysis of metabolic reprogramming and IGF-1 modulation in SCA3 transgenic mice

status: Public on Aug 11 2021

city: Changhua

first: Chin-San

last: Liu

address: 135 Nan-Hsiao Street

country: Taiwan

institute: Changhua Christian Hospital

summary: Spinocerebellar ataxia type 3 (SCA3), also called Machado-Joseph disease (MJD), is a polyQ neurodegenerative disease that is still seeking cure. We used SCA-3 84Q transgenic mice as a disease model to study the therapeutic effect of insulin-like growth factor 1 (IGF-1). Transcriptomic and metabolomic profiles were established and compared  between the control (15Q), disease(84Q) and treatment(84Q+IGF-1) groups using RNA-seq and metabolic network analysis.  SCA3-84Q mice showed a decrease in glycolysis, lipolysis and mitochondrial oxidative phosphorylation, and an increase in apoptosis, and IGF-1 treatment reversed the alterations slightly.

overall_design: RNAseq analysis of cerebellar tissue from three groups of mice, each group contains 3 replicates. 15Q mice are used as control samples, 84Q mice are disease samples and 84Q mice treated with IGF1 are belong to treatment samples.

first: Yu-Te

last: Lin

first: Yong-Shiou

first: Wen-Ling

last: Cheng

first: Jui-Chih

last: Chang

first: Yi-Chun

last: Chao

first: An-Chi

last: Wei


title: RIPK1 kinase-dependent gene expression in mouse microglia and astrocytes in vivo during EAE

first: Dimitry

last: Ofengeim

summary: To determine the role of RIPK1 kinase signaling in microglia and astrocytes during EAE (mouse model of MS), we extracted spinal cords of naive, EAE-vehicle and EAE mice treated with RIPK1 kinase inhibitor (GSK’547) for transcript profiling using RNAseq. We identify various genes that are differentially expressed in EAE disease compared to naive mice, and a subset of these are modulated in a RIPK1 kinase-dependent manner in both astrocytes and microglia. The top RIPK1 kinase-dependent gene pathways include oxidative phosphorylation and mitochondrial dysfunction in microglia and EIF2 signaling and cholesterol biosynthesis in astrocytes. This study demonstractes critical and distinct roles for RIPK1 kinase signaling in both microglia and astrocytes during EAE

overall_design: Examination of spinal cord astrocytes and microglia from 4 naïve, 6 EAE-vehicle and 5 EAE-RIPK1 inhibitor (GSK'547)-treated mice

first: Zelic

last: Matija

first: Zhu

first: Xia

last: Tai-he

first: Degterev

last: Alexei

first: Keane

last: Aislinn

first: Ofengeim

last: Dimitry


title: JHMV-specific Treg memory

city: Coralville

first: Alan

middle: Jacob

last: Sariol

state: IA

address: 2868 Coral Ct., Apt 201

department: Microbiology and Immunology

institute: University of Iowa

summary: Regulatory T cells (Tregs) are critical for regulating immunopathogenic responses in a variety of infections, including infection of mice with JHMV, a neurotropic coronavirus that causes immune-mediated demyelinating disease. While virus-specific Tregs are known to mitigate disease in this infection by suppressing pathogenic effector T cell responses of the same specificity, it is unclear if these virus-specific Tregs form memory populations and persist similar to their conventional T cell counterparts of the same epitope specificity. Using congenically labeled JHMV-specific Tregs, we found that virus-specific Tregs persist long-term after infection, through at least 180 days post-infection. We additionally demonstrate that these cells are better able to proliferate after infection than naïve Tregs of the same specificity, further suggesting that these cells differentiate into memory Tregs upon encountering cognate antigen. Together, these data suggest that virus-specific Tregs are able to persist long-term in the absence of viral antigen as memory Tregs.

overall_design: We used RNA-seq to analyze FACS-sorted virus-specific Tregs from naïve mice and 60 day post-JHMV infection mice, n=4 mice per group

first: Stanley

last: Perlman


title: RNA-seq for paired maternal blood, cord blood, and placenta

city: Lebanon

first: Caitlin

middle: G

last: Howe

state: NH

address: 1 Medical Center Dr

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

summary: We generated RNA-seq data for 60 maternal blood white blood cells collected in the first trimester of pregnancy and 57 paired cord blood white blood cells

overall_design: RNA-seq for maternal blood


title: Detection Novel miRNA Potentially Involved in Proximal Tubules under Hypoxia Using Next-Generation Sequencing and Bioinformatic Approaches

city: Kaohsiung

last: Tsai

address: No.100 , Tzyou 1st Road

institute: Kaohsiung Medical University

summary: MicroRNAs are hypothesized to play critical roles in the regulation ofhypoxia-induced proximal tubular injury. The aim of this study is to explore novel microRNAs differentially expressed in HK-2 cells under normoxia and hypoxia conditions. RNAs were extracted from HK-2 cells cultured under normoxia and hypoxia for sequencing. Using the next generation sequencing and bioinformatics approaches, we identified 11 differentially expressed microRNAs in HK-2 cells under hypoxia condition.

overall_design: Next-generation sequencing for small RNA of HK-2 cells under normoxia and hypoxia conditions.

first: Mei-Chuan

last: Kuo

first: Ya-Ling

last: Hsu


title: Mammalian apoptotic factors regulate bacterial gene expression II

first: Justin

last: Perry

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: The experiment consisted of two conditions: Salmonella grown in fresh culture media  or UV irradiation induced apoptotic supernatants. Each condition consisted of four biological replicates.

first: Christopher

last: Anderson

last: Medina

first: Brady

last: Barron

first: Laura

last: Karvelyte

first: Tania

last: Aaes

first: Irina

last: Lambertz

first: Parul

last: Mehrotra

first: Amanda

last: Goncalves

first: Kelly

last: Lemeire

first: Gillian

last: Blancke

first: Vanessa

last: Andries

first: Farzaneh

last: Ghazavi

first: Arne

last: Martens

first: Geert

last: van Loo

first: Lars

last: Vereecke

first: Peter

last: Vandenabeele

first: Kodi

last: Ravichandran


title: Proof of Gene Doping in a Mouse Model with a Human Erythropoietin Gene Transferred Using an Adenoviral Vector

city: Tsukubashi

first: Takeito

last: Sugasawa

state: Ibarakiken

address: Igakukei Gakukeitou 236, 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

summary:
Gene doping model by hEPO (human erythropoietin) and adenoviral vector was established in the study.
This study revealed that the gene expression profile in whole blood on the gene doping model significantly altered, which may be a new marker of hEPO-gene doping

overall_design: Whole blood in the model and control mice were analyzed using total RNA-seq.

first: Takehito


title: Transcriptome analysis of Paracoccus denitrificans following exposure to hexavalent chromium under aerobic and anoxic conditions

city: Hayward

first: Fatemeh

last: Shirazi

address: 26229 Eden Landing Rd.

institute: Microvi Biotech Inc.

summary: Suspended cell studies were performed to document whole-genome transcriptional profiles as a function of Cr(VI) reduction under different electron accepting conditions. Cell suspension studies were performed in 250 mL serum bottles for two conditions: 1) under anoxic condition with lactate as carbon source and nitrate as electron acceptor, and 2) under aerobic condition with lactate as carbon source and oxygen as electron acceptor. The initial Cr(VI) and nitrate concentrations were 1000 μg/L and 40 mg N/L, respectively. Samples from both the conditions were collected after 5 hours and the cell pellet was saved at -80°C.

overall_design: Two samples were analyzed which were exposed to different conditions for Cr(VI) reduction

first: Ameen

last: Razavi


title: RIPK1 kinase-dependent gene expression in mouse microglia and astrocytes in vitro

first: Dimitry

last: Ofengeim

summary: To determine the role of RIPK1 kinase-dependent transcriptional signaling in microglia and astrocytes, we stimulated cells with RIPK1 kinase-activating stimuli TNF/5z-7 and TNF/Smac/zVAD in the presence or absence of the RIPK1 kinase inhibitor Nec-1s. We identified various genes modulated in a RIPK1 kinase-dependent manner with each stimulation in both microglia and astrocytes, and the main biological pathways were related to an inflammatory and immune response. We identified many cytokines and chemokines upregulated in both microglia and astrocytes upon RIPK1 kinase activation, demonstrating the contribution of RIPK1 kinase signaling to pro-inflammatory responses in microglia and astrocytes

overall_design: 4 biological replicates of mouse microglia were treated with (1) DMSO, (2) Nec-1s, (3) TNF/5z-7, (4) TNF/Smac/zVAD, (5) TNF/5z-7/Nec-1s, and (6) TNF/Smac/zVAD/Nec-1s; 3 replicates of astrocytes were treated with (1) DMSO, (2) Nec-1s, (3) TNF/Smac/zVAD, (4) TNF/Smac/zVAD/Nec-1s

first: Zelic

last: Matija

first: Zhu

last: Cheng

first: Xia

last: Tai-he

first: Ofengeim

last: Dimitry


title: Genome-wide contacts of rDNA units detected by 4C procedure in human genome [hESM01]

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: 4C-rDNA procedure was used for analysis of genomic contacts of rDNA units in hESM01 cells. The primers for 4C were selected downstream from EcoRI site at coordinate  30487 in rDNA sequence with Accession number U13369.1.

overall_design: Analysis of rDNA genome-wide contacts in hESM01 cells using 4C approach.

first: Yuri

middle: V

last: Kravatsky

first: Olga

last: Kretova


title: Super-enhancer based development of an endothelial specific lentiviral vector

city: Kuopio

first: Minna

last: Kaikkonen-Määttä

country: Finland

institute: A. I. Virtanen Institute

summary: Hypoxia-regulated endothelial-specific lentiviral vector that can be used for endothelial-targeted gene therapy.

overall_design: Construction of Lentiviral vectors containing endothelial-specific enhancer driving expression of reporter gene, vectors evaluation in vitro and Knock out validation studies with CRISPR/Cas9, followed by RNA-Seq in EA.hy926.

first: N

last: Laram-Karam

first: I

last: Mushimiyimana

first: M

first: H

last: Niskanen

first: S

last: Ylä-Herttuala


title: Somatic piRNAs in veterbrate kidney

city: Rochester

first: Xin

last: Li

address: 602 Elmwood Drive

institute: University of Rochester

summary: SmallRNA seq and longRNA seq of chicken kidney and testis

overall_design: High-throughput sequencing data including RNAseq and small-RNA seq of chicken kidney and testis. All sequencing data were sequenced on Illumina platform.

middle: Z

first: Rudo

last: Ndamba


title: Time-course study of microarray transcriptome analysis in influenza virus-infected MDCK and TR7 cells.

city: Yahaba-cho

first: Reiko

last: Tsutsumi

state: Iwate Prefecture

address: Idaidori 1-1-1

institute: Iwate Medical University

summary: Comparative transcriptome analysis indicated that expression of apoptosis-related MX1 and MMP9 was suppressed in TR7 cells both before and during viral infection. Meanwhile, CDKN2A was upregulated in TR7 cells, and CCND3 and CASP7 were upregulated in MDCK cells, which supported that cell cycle arrest in TR7cells benefited influenza virus production.

overall_design: MDCK and TR7 cells were either infected with A/Panama/H3N2 or mock infected with PBS. The purpose of this study is to show the difference in RNA expression in both cultured cells over time by microarray analysis.

first: Daisuke

last: Minegishi

first: Shigehiro

last: Sato


title: Genome-wide DNA methylation profiling in human semen samples

city: Krakow

first: Aleksandra

last: Pisarek-Pacek

state: Malopolska

address: Gronostajowa 7A

department: Malopolska Centre of Biotechnology

country: Poland

institute: Jagiellonian University

type: Methylation profiling by genome tiling array

summary: DNA methylation analysis using the Infinium MethylationEPIC BeadChip arrays was applied to 40 semen-derived DNA samples (age range 24 – 58 years). The aim of the study was to discover differentially methylated sites (DMS) that correlate with age.

overall_design: 40 semen samples were analysed using the Infinium MethylationEPIC BeadChip arrays.

first: Wojciech

last: Branicki


title: Ypel4-null Mice Display Secondary Polycythemia Associated with Ovalocytosis and Lower Band 3 Protein Levels on Red Blood Cells

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

summary: The YPEL family genes are highly conserved across a diverse range of eukaryotic organisms and thus potentially involved in essential cellular processes. Ypel4, one of five YPEL family gene orthologs in mouse and human, is highly and specifically expressed in late terminal erythroid differentiation. In this study, we investigated the role of Ypel4 in murine erythropoiesis, providing for the first time an in-depth description of a Ypel4-null phenotype in vivo. We demonstrated that the Ypel4-null mice displayed a secondary polycythemia with macro- and reticulocytosis. While lack of Ypel4 did not affect steady-state erythropoiesis in the bone marrow or spleen, the anemia-recovering capacity of Ypel4-null cells was diminished. Furthermore, Ypel4-null red blood cells (RBC) were cleared from the circulation at an increased rate, demonstrating an intrinsic defect of RBCs. Scanning electron micrographs revealed an ovalocytic morphology of Ypel4-null RBCs and functional testing confirmed reduced deformability. Even though Band 3 protein levels were shown to be reduced in Ypel4-null RBC membranes, we could not find support for a physical interaction between YPEL4 and the Band 3 protein. In conclusion, our findings provide crucial insights into the role of Ypel4 in preserving normal red cell membrane functionality.

overall_design: For RNA-seq, polychromatic and orthochromatic erythroblasts in Ypel4+/+ and Ypel4-/- bone marrow were sorted and sequenced in quadriplicates.

first: Alexander

last: Mattebo

first: Taha

last: Sen

first: Maria

last: Jassinskaja

first: Kristýna

last: Pimková

first: Isabel

last: Prieto González-Albo

first: Abdul

last: Ghani Alattar

first: Ramprasad

last: Ramakrishnan

first: Stefan

last: Lang

first: Marcus

last: Järås

first: Jenny

last: Hansson

first: Sofie

last: Singbrant

first: Emile

last: van den Akker

first: Johan

last: Flygare


title: Long Noncoding RNA RP11-115N4.1Promotes Inflammatory Responses by Interacting with HNRNPH3 and Enhancing the Transcription of HSP70 in Unexplained Recurrent Spontaneous Abortion

city: Guangzhou

first: Meilan

last: Liu

address: Yanjiang Weat Road 107

department: Obstetrics and Gynecology

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: RP11-115N4.1 was identified as the most differentially expressed lncRNA which was highly upregulated in peripheral blood of non-pregnant URSA patients (P = 3.63E-07, Fold change = 2.96),andthis dysregulation was further validated in approximately 26.7% additional patients (4/15). RP11-115N4.1 expression was detected in both lymphocytes and monocytes of human peripheral blood, andin vitro overexpression of RP11-115N4.1 decreased cell proliferation in K562 cellssignificantly. Furthermore, heat-shock HSP70 genes (HSPA1A and HSPA1B) were found to be significantly upregulated upon RP11-115N4.1 overexpression by transcriptome analysis (HSPA1A (P = 4.39E-08, Fold change = 4.17), HSPA1B (P = 2.26E-06, Fold change = 2.99)).RNApull down and RNA immunoprecipitation assay (RIP) analysis demonstrated that RP11-115N4.1 bound to HNRNPH3 protein directly, which in turn activateheat-shock proteins (HSP70) analyzed by protein-protein interaction and HNRNP` knockdown assays. Most importantly,the high expression of HSP70 was also verified in the serum of URSA patients and the supernatant of K562 cells with RP11-115N4.1 activation, andHSP70 in supernatant can exacerbate inflammatory responses in monocytes by inducing IL-6, IL-1β and TNF-α and inhibit the migration of trophoblast cells, which might associate with URSA.

overall_design: We profiled lncRNAs expression in peripheral blood from 5 non-pregnant URSA patients and 5 matched controls by lncRNA microarray analysis. Functions of URSA-associated lncRNAs were further investigated in vitro.

first: Xiaoyue

last: Sun

first: Liqiong

last: Zhu

first: Menglan

first: Kewen

last: Den

first: Xiaolu

last: Nie

first: Hanjie

last: Mo

first: Tao

last: Du

first: Bingqian

last: Huang

first: Lihao

last: Hu

first: Liuhong

last: Liang

first: Dongyan

last: Wang

first: Yinger

last: Luo

first: Jinling

last: Yi

first: Jianping

last: Zhang

first: Xingming

last: Zhong

first: Chunwei

last: Cao

first: Hui

last: Chen


title: Identification of the genes are directed by GPR43

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Modulation of GPR43 activity affected the expression level of YAP/TAZ target genes

overall_design: GPR43 expressing HEK293 cells were treated DMSO as control, acetate, and CATPB for 90min.

first: Bi-Oh

last: Park

first: Sunhong

first: Jong-Hwan

first: Seon-Young


title: RNA-seq analysis of pathogen and host in the early stages of Plague pulmonary infection using a novel dual RNA extraction method

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

summary: The goal of this study is to determine the host and pathogen transcriptomic response during pneumonic plague infection.  Mice were infected intranasally with high dose of 800,000 cfu/mouse (1500 LD50). Mice were sacrificed at 1, 24 and 48 hours post infection and dual RNA was extracted. In order to isolate high quantities of superior quality mRNA from bacteria and mice we used a novel technique, that employed infusion of an RNA preserving reagent (RNAlater) into the lungs of the animals through the trachea under deep anesthesia prior to the collection of the organs. Unprecedently, this method enables isolation of stable dual mRNA from lungs of mice infected with Y. pestis, as early as 24 hours post infection. RNA-seq libraries were generated and sequencing of 100bp paired-end was performed on the Illumina NovaSeq 6000 system. The RNA was used for transcriptomic analyses which provided a comprehensive gene-expression profile of both the host and pathogen at 24 and 48 hours post infection.

sample_organism:
Yersinia pestis
Mus musculus

platform_organism:
Yersinia pestis
Mus musculus

overall_design: Examination of dual RNA extracted from lungs of mice infected with Y. pestis + samples collected from uninfected mice (naïve) and samples of Y. pestis grown in liquid culture (=17 samples).

first: Ofir

last: Israeli

last: Cohen-Gihon

first: Moshe

last: Aftalion

first: David

last: Gur

first: Yaron

last: Vagima

first: Ayelet

last: Zauberman

first: Yinon

last: Levy

first: Anat

last: Zvi

first: Theodor

last: Chitlaru

first: Emanuel

last: Mamroud

first: Avital

last: Tidhar


title: The Tumor Microenvironment Shapes Innate Lymphoid Cells in Patients with Hepatocellular Carcinoma

city: Bethesda

first: Amanda

last: Craig

state: Maryland

address: 37 Convent Dr. Bld.37/Rm.3044

institute: National Institutes of Health

summary: Objective: Hepatocellular carcinoma (HCC) represents a typical inflammation-associated cancer. Tissue resident innate lymphoid cells (ILCs) have been suggested to control tumor surveillance. Here we studied how the local cytokine milieu controls ILCs in HCC. Design: We performed bulk RNA sequencing of HCC tissue as well as flow cytometry and single-cell RNA sequencing of enriched ILCs from non-tumor liver, margin and tumor core derived from 48 HCC patients. Simultaneous measurement of protein and RNA expression at the single-cell level (AbSeq) identified precise signatures of ILC subgroups. In-vitro culturing of ILCs was used to validate findings from in-silico analysis. Analysis of RNA-sequencing data from large HCC cohorts allowed stratification and survival analysis based on transcriptomic signatures. Results: RNA sequencing of tumor, non-tumor and margin identified tumor-dependent gradients of which were not only associated with poor survival but also control ILC plasticity. Single-cell RNA sequencing and flow cytometry of ILCs from HCC livers identified NK-like cells in the non-tumor tissue, losing their cytotoxic profile as they transitioned into tumor ILC1 and NK-like-ILC3 cells. Tumor ILC composition was mediated by cytokine gradients that directed ILC plasticity towards activated tumor ILC2s. This was liver-specific and not seen in ILCs from PBMC. Patients with high ILC2/ILC1 ratio expressed IL-33 in the tumor that promoted ILC2 generation which was associated with better survival.  Conclusion: Our results suggest that the tumor cytokine milieu controls ILC composition and HCC outcome. Specific changes of cytokines modify ILC composition in the tumor by inducing plasticity and alter ILC function.

overall_design: 58 liver tissue samples from patients with HCC

first: Bernd

last: Heinrich

first: Tim

middle: F

last: Greten

first: Firouzeh

last: Korangy


title: Inhibition of epigenetic modifiers LSD1 and HDAC1 blocks rod photoreceptor death in mouse models of Retinitis Pigmentosa.

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: In retinitis pigmentosa mouse models inhibitors of histone modification enzymes LSD1and HDAC1 blocked rod degeneration, preserved vision and affected the expression of multiple genes including maintenance of rod-specific transcripts and downregulation those involved in inflammation, gliosis and cell death.

overall_design: Total 11 samples of mouse retina at PN24: 2 wild type controls C57Bl/6J, 3 rd10 B6.CXB1-Pde6brd10/Jrd10, 3 wild type treated with GSK2879552 (LSD1 inhibitor) from PN9 till PN24 and 3 rd10 treated with GSK2879552  from PN9 till PN24

first: Evgenya

middle: Y

last: Popova

last: Imamura

first: Samuel

last: Zhang

first: Colin

last: Barnstable


title: Genome-wide contacts of rDNA units detected by 4C procedure in human genome [K562]

first: Nickolai

last: Tchurikov

summary: 4C-rDNA procedure was used for analysis of genomic contacts of rDNA units in K562 cells.

overall_design: Analysis of rDNA genome-wide contacts in K562 cells using 4C approach.

first: Yuri

last: Kravatsky

first: Olga

last: Kretova


title: Mechanisms of impaired lung development and ciliation in Mannosidase-1-alpha-2 (Man1a2) mutants

city: La Jolla

first: Kim

last: Ngo

address: 9500 Gilman Drive #0412

department: Department of Bioengineering

institute: University of California, San Diego

summary: Ciliary defects cause heterogenous phenotypes related to mutation burden which lead to impaired development. A previously reported homozygous deletion in the Man1a2 gene causes lethal respiratory failure in newborn pups and decreased lung ciliation compared with wild type (WT) pups. The effects of heterozygous mutation, and the potential for rescue are not known. Purpose: We hypothesized that survival and lung ciliation a) would decrease progressively in Man1a2 +/- heterozygous and Man1a2 -/- null newborn pups compared with WT, and b) could be enhanced by gestational treatment with N-Acetyl-cysteine (NAC), an antioxidant.  Methods: Man1a2 +/- adult mice were fed NAC or placebo from a week before breeding through gestation. Survival of newborn pups was monitored for 24 hours. Lungs, liver and tails were harvested for morphology, genotyping and transcriptional profiling. Results: Survival (p=0.0001, Kaplan-Meier) and percent lung ciliation (p=0.0001, ANOVA) measured by frequency of Arl13b+ respiratory epithelial cells decreased progressively, as hypothesized. Compared with placebo, gestational NAC treatment enhanced a) lung ciliation in pups with each genotype, b) survival in heterozygous pups (p=0.017) but not in WT or null pups. Whole transcriptome of lung but not liver demonstrated patterns of up- and down-regulated genes that were identical in living heterozygous and WT pups, and completely opposite to those in dead heterozygous and null pups. Systems biology analysis enabled reconstruction of protein interaction networks that yielded functionally relevant modules and their interactions. In these networks, the mutant Man1a2 enzyme contributes to abnormal synthesis of proteins essential for lung development. The associated unfolded protein, hypoxic and oxidative stress responses can be mitigated with NAC. Comparisons with the developing human fetal lung transcriptome show that NAC likely restores normal vascular and epithelial tube morphogenesis in Man1a2 mutant mice. Conclusions: Survival and lung ciliation in the Man1a2 mutant mouse, and its improvement with N-Acetyl cysteine is genotype-dependent. NAC-mediated rescue depends on the central role for oxidative and hypoxic stress in regulating ciliary function and organogenesis during development

overall_design: Total RNA samples from explanted lung and liver tissue from each of NAC and Placebo groups were pooled from 3 independent experiments per pool from alive WT, alive Man1a2 heterozygous, dead Man1a2 null, and 2 samples per pool for dead Man1a2 heterozygous pups.

first: Mylarappa

last: Ningappa

first: Morayooluwa

last: Adenuga

first: Nada

last: Mohamed

first: Tejaswini

last: Narayanan

first: Krishna

last: Prasadan

first: Chethan

last: Ashokkumar

first: Jishnu

last: Das

first: Lori

last: Schmitt

first: Miguel

last: Reyes-Mujica

first: George

last: Gittes

first: Cecilia

last: Lo

first: Shankar

last: Subramaniam

first: Rakesh

last: Sindhi


title: Transcriptomic analysis of MYC-inhibited Medulloblastoma-derived D283 Med cells

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

summary: Medulloblastoma is one of the most common malignant pediatric brain tumors. Group 3 is the most aggressive molecular subgroup, showing the highest rate of metastasis at diagnosis. To date, very few long noncoding RNAs have been implicated in Group 3 Medulloblastoma biology. Here, we identified the long noncoding RNAs dependent on the activity of the MYC oncogene, the major driver gene of Group 3 Medulloblastoma.

overall_design: 4 RNA samples derived from MYC-inhibited D283 Med cells and 4 control samples derived from untreated D283 Med cells were subjected to RNA-Seq analysis.

first: Jessica

last: Rea

first: Pietro

last: Laneve

first: Elisa

last: Caffarelli


title: Protein Arginine Methyltransferase 1 is Essential for the Meiosis of Male Germ Cells

first: Byoung-Ha

last: Yoon

address: Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

institute: KRIBB

summary: Methods: Prmt1 floxed mice were crossed with Rip2-Cre and Pdx1-CreERT2 mice to generate Prmt1 KO and Prmt1 iKO mice. R26-eYFP mice were crossed for lineage tracing experiments and  cell sorting. All mice were backcrossed and maintained on a C57BL/6J background. Cre recombination for CreERT2 was induced by total 5 times intraperitoneal injections (75 mg/kg) of corn oil dissolved tamoxifen (T5648, Sigma-Aldrich) over 2 weeks.

overall_design: mRNA profiles of wild type (WT) and Prmt1 -/- mice were generated by deep sequencing, in duplicate, using Illumina Hiseq.

first: Keesook

last: Lee

first: Mirang

last: Kim


title: Adult Phenotypes and Gene Expression in the Brain at Single Cell Resolution After Developmental Alcohol Exposure in Drosophila

city: Greenwood

first: Vijay

last: Shankar

state: South Carolina

address: 115 Milford Pines Drive

institute: Clemson University

summary: Fetal alcohol exposure can lead to developmental abnormalities, intellectual disability, and behavioral changes, collectively termed fetal alcohol spectrum disorder (FASD). In 2015, the CDC found that 1 in 10 pregnant women report alcohol use and more than 3 million women in the USA are at risk of exposing their developing baby to alcohol. Identifying genetic risk alleles for FASD is challenging, since time, dose and frequency of exposure are often unknown, and phenotypic manifestations of FASD are diverse and become evident long after exposure. Drosophila melanogaster presents an excellent model to study developmental effects of alcohol exposure, because virtually unlimited numbers of individuals of the same genotype can be reared rapidly and economically under well-controlled environmental conditions without regulatory restrictions.  Furthermore, flies exposed to alcohol undergo physiological and behavioral changes that resemble human alcohol-related phenotypes. Flies reared on ethanol-supplemented medium show decreased viability, reduced sensitivity to ethanol, and disrupted sleep and activity patterns. To assess alcohol-modulated gene expression in the brains of flies reared on alcohol, we performed single cell RNA sequencing and resolved cell clusters with differentially expressed genes representing distinct neuronal and glial populations. We observed extensive sexual dimorphism. Two clusters associated with glial biomarkers showed greater differential gene expression in males, whereas mushroom body-derived cells exhibited a greater degree of differential gene expression in females.  Results obtained from these studies provide a blueprint for translational studies on alcohol-induced effects on gene expression in the brain that may contribute to or result from FASD in human populations.

overall_design: single-cell RNA-seq profiling of 8 samples consisting of 20 Drosophila brains each, 2 conditions (reference and alcohol supplemented growth media), 2 sexes (male and female) and 2 replicates

first: Sneha

last: Mokashi

first: Rebecca

last: MacPherson

first: Rachel

last: Hannah

first: Trudy

last: Mackay

first: Robert

last: Anholt


title: Melatonin promotes Arabidopsis root growth in an IAA dependent manner [7d]

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

summary:
Purpose: We aimed to compare transcriptomic changes after melatonin (MT) and IAA treatments in Arabidopsis and dissected cross-talk between MT and IAA
Methods: A total amount of 1 μg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq2000 platform and paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0).
Results:In total, six samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis identified coregulated genes by melatonin and IAA in Arabidopsis seedlings

overall_design: In this study, transcriptome changes after 1nM IAA and 10nM MT were compared at 7d after treatment. The rosette leaves from control and treated plants were collected for RNA isolation. Three treatments in duplicate were used in this study.

first: Li

last: Yang


title: Genome-wide DNA methylome analysis identifies putative biomarkers associated with the survival of human ovarian cancers

city: Pokfulam

first: David

middle: Wai

state: Hong Kong

address: L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road

department: Obs. & Gyn.

country: Hong Kong

institute: The Uniersity of Hong Kong

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: The histone variant H3.3 promotes the active chromatin state to repress flowering in Arabidopsis

city: Beijing

first: Fengyue

last: Zhao

address: No. 1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Genetics and Developmental Biology Chinese Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report that H3.3 stimulates the expression of FLC and its homologs, and promotes the active histone modifications at their loci. FRI directly interacts with the H3.3 chaperone HIRA and elevates H3.3 deposition towards the FLC 3’ region. The enriched H3.3 facilitates FLC 3’ end interaction with the 5’ end, promoting active histone modifications around the transcription start site (TSS) of FLC. In contrast, though coordinately activate FLC expression; H3.3 and H2A.Z antagonize each other at the FLC chromatin. In addition to FLC and its homologs, H3.3 is required for H3K4me3 at a subset of especially short genes. Our findings reveal the important function of H3.3 in the regulation of the active chromatin state, which enhances FLC transcription and floral repression

overall_design: HTR5 distribution in seedlings

first: Danhua

last: Jiang

first: Huairen

last: Zhang


title: Genome-wide DNA methylome analysis identifies putative biomarkers associated with the survival of human ovarian cancers [80 cases]

summary: We conducted an epigenome-wide association study (EWAS) to evaluate global DNA methylation in EOC. In a retrospective cohort of 80 primary ovarian cancers, we observed that global DNA hypermethylation was significantly associated with high-grade tumors, platinum-resistance and poor prognosis. We determined that 8,600 differentially methylated probes (DMPs) were enriched in the intergenic regions of 4,673 genes involved in small GTPases and were significantly correlated with the PI3K-AKT, MAPK, RAS, and WNT oncogenic pathways.

overall_design:
Whole-genome DNA methylation analysis was performed on a retrospective cohort of 80 patients with mixed tumor subtypes, gradings and stages of epithelial ovarian cancers.
contributor: Centre for PanorOmic Sciences (CPOS), Genomics Core, HKU


title: Bile acid therapeutics for NASH

city: Oklahoma City

last: Sharp

state: OK

address: 975 NE 10th St.

country: USA

institute: University of Oklahoma

summary: We studied the effect of AAV8-TBG-FGF15 and GSK2330672 (8mg/kg/day), alone or in combination, against diet-induced NASH and fibrosis in mice

overall_design: Male C57BL/6J mice were fed chow or high fat (40% Kcal), high cholesterol (2%) and high fructose (20%) (HFCFr) diet for 32 weeks (Research Diet Inc.). AAV8-TBG-FGF15 (tail vein injection) and GSK2330672 (8 mg/kg/day, mixed with diet) treatment were initiated after 20 weeks of HFCFr diet feeding. Each experimental group contains 5 mice.

first: Tiangang

last: Li

last: Matye

first: Kenneth

last: Jones


title: RNase III and RNase E influence post-transcriptional regulatory networks involved in virulence factor production, metabolism and regulatory RNAs processing in Bordetella pertussis.

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

country: Canada

institute: Simon Fraser University

summary: Bordetella pertussis has been shown to encode regulatory RNAs, yet the post-transcriptional regulatory circuits on which they act remain to be fully elucidated. We generated mutants lacking the endonucleases RNase III and RNase E and assessed their individual impact on the B. pertussis transcriptome. RNA-Seq analysis showed differential expression of ~25% of the B. pertussis transcriptome in each mutant with only 28% overlap between data sets. Both endonucleases exhibited substantial impact on genes involved in amino acid uptake e.g. ABC transporters, and in virulence e.g. the type III secretion system, and the autotransporters vag8, tcfA and brkA. Interestingly, mutations in RNase III and RNase E drove the stability of many transcripts, including those involved in virulence, in opposite directions; a result that was validated by qPCR and immunoblot for tcfA and brkA. Of note, whereas similar mutations to RNase E in E. coli have subtle effects on transcript stability, a striking >20-fold reduction in four gene transcripts, including tcfA and vag8, was observed in B. pertussis. We further compared our data set to the regulon controlled by the RNA chaperone Hfq to identify B. pertussis loci influenced by regulatory RNAs. This analysis identified ~120 genes and 19 operons potentially regulated at the post-transcriptional level. Thus, our findings revealed how changes in RNase III- and RNase E-mediated RNA turnover influence pathways associated with virulence and cellular homeostasis. Moreover, we highlighted loci potentially influenced by regulatory RNAs, providing insights into the post-transcriptional regulatory networks involved in fine tuning B. pertussis gene expression.

overall_design: A total of 15 samples, representing three genotypes (wild type and two mutants), with five replicates each.

first: Gyles

last: Ifill

first: Amy

middle: H

last: Lee

first: George

last: Mackie

first: Qing

last: Chen

first: Scott

last: Stibitz

last: Hancock

last: Fernandez


title: Hippocampal transcriptome changes after subarachnoid hemorrhage in mice

city: Houston

first: Angelique

last: Regnier-Golanov

state: United States of America

address: 6560 Fannin St #900

department: Neurosurgery

institute: The Houston Methodist Neurological Institute

summary: Purpose: Subarachnoid hemorrhage (SAH) is fatal in approximately 40% of cases. However, among survivors up to 95% experience permanent disabilities: post-SAH syndrome, which include impaired memory, executive functions, emotional and cognitive disturbances. Up to 45% of SAH patients are unable to continue with their professional activities. The long-term cognitive deficits result from morphological brain damage, including atrophy of the temporomesial/hippocampal area, which correlates with decreased neurocognitive scores. The mechanisms of the remote brain damage following SAH remain unknown, which hinders the progress in identifying new therapeutic targets. To unveil the leading mechanisms of permanent cognitive abnormalities following SAH and origin of atrophy of the temporomesial/hippocampal area, we analyzed SAH-induced specific hippocampal genomic pathways, which may lead to long term morphological damage.  methods: Hippocampal RNA of SAH and Control groups, obtained 4 days after SAH induced by perforation of the circle of Willis in mice, was processed and sequenced. Using the next-generation RNA sequencing we determined differentially expressed genes in the bilateral whole hippocampus remote from SAH and applied different functional analyses and clustering tools to determine the main molecular pathways.   Results: Differential gene expression analysis detected 642 upregulated and 398 down-regulated genes (false discovery rate <0.10) in SAH compared to Control group. Functional analyses using IPA suite, Gene Ontology terms, REACTOME pathways, and MsigDB Hallmark gene set collections revealed suppression of oligodendrocytes/myelin related genes, and overexpression of genes related to complement system along with genes related to innate and adaptive immunity, and extracellular matrix reorganization. Interferon regulatory factors, TGF-β1 and BMP, were identified as major orchestrating elements in the hippocampal tissue response. The MEME-Suite identified binding motifs of Krüppel-like factors, zinc finger transcription factors, and interferon regulatory factors as overrepresented DNA promoter motifs.   Conclusion: Our findings suggest that damage of the entorhinal cortex by the subarachnoid blood remotely triggers specific hippocampal response, which may include suppression of oligodendrocytes functioning due to anterograde degeneration of hippocampal afferents accompanied. Identification of the prominent molecular hippocampal pathways may lead to the development of new therapeutic approaches for the treatment of long-term SAH consequences.

overall_design: Transcriptomic analysis, using bulk mRNAseq, of bilateral whole mouse hippocampus at 4-days  after Naïve, Sham-operated or Subarachnoid hemorrhage induced by the model of unilateral monofilament perforation of  the circle of Willis.

first: A

first: F

last: Dündar

first: P

last: Zumbo

first: D

last: Betel

first: M

last: Hernandez

first: L

middle: E

last: Peterson

first: E

last: Lo

last: Golanov

first: G

middle: W

last: Britz


title: Pathway conversion enables a double-lock mechanism to maintain DNA methylation and genome stability

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

institute: Karolinska institute

type: Methylation profiling by high throughput sequencing

type: Genome variation profiling by high throughput sequencing

summary: The CMT2 and RNA-directed DNA methylation (RdDM) pathways have been proposed to separately maintain CHH methylation in specific regions of the Arabidopsis thaliana genome. Here, we show that dysfunction of the chromatin remodeller DDM1 causes hundreds of genomic regions to switch from CMT2-dependency to RdDM-dependency in DNA methylation. These converted loci are enriched at the edge regions of long transposable elements (TEs). Furthermore, we found that blocking the pathway switch by disrupting both DDM1 and RdDM causes strong reactivation of TEs and a burst of TE transposition in the first generation of mutant plants, indicating that the pathway conversion is critical to maintaining TE repression and protecting genomic stability. Our findings reveal the existence of a novel pathway conversion-based backup mechanism to guarantee the maintenance of DNA methylation and genome integrity.

overall_design: To investigate potential genetic interactions between the CMT2 and RdDM pathways, we generated single-base resolution maps of the DNA methylomes of the nrpd1, nrpe1, cmt2, ddm1, ddm1nrpd1, ddm1nrpe1, and ddm1cmt2 mutants, RNA sequencing  in ddm1, ddm1nrpd1, ddm1nrpe1, and ddm1cmt2 mutants, resequencing in ddm1, nrpd1 and ddmcmt2.

first: Li

last: He

first: Chen

first: Qingzhu

last: Zhang

first: Gaurav

last: Zinta

first: Dong

last: Wang

first: Rosa

last: Lozano-Durán

first: Jian-Kang

last: Zhu


title: Single cell RNA sequencing reveals cellular heterogeneity of PBMC of systemic lupus erythematosus patients

first: Yiyao

last: Deng

state: China

address: Department of Nephrology

department: Department of Nephrology

institute: Chinese PLA General Hospital

summary: To investigate ISGs expression chracteristics of leucocyte types of SLE patients, single cell RNA sequencing was applied to 2 SLE patients and 1 health volunteer.

overall_design: 10X Genomics single cell RNA sequencing was applied to PBMC of 2  SLE new onset patients without using any immunosupressive drugs and 1 health volunteer.

first: Xiangmei

last: Chen


title: Reprogramming of glucocorticoid receptor function by hypoxia: RNA-seq after 2h in the hypothalamus

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: Glucocorticoids (GCs) are the most important stress hormones. They act via the GC receptor GR (encoded by the Nr3c1 gene). Their role is to control metabolic pathways, and to limit inflammation. The latter is often compromised, by unknown mechanisms, in severe inflammatory conditions. We here investigated the in vivo impact of hypoxia on GR function in mice, by genome wide analysis in liver and by means of deep hypoxia. Our data reveal that hypoxia leads to profound reductions in transcriptional output of GR, when stimulated with dexamethasone, leading to absent induction of genes with anti-inflammatory functions such as Tsc22d3 and Dusp1 in liver and other organs. Hypoxia also activates the entire HPA axis, by HIF1α and HIF2α activation in hypothalamus, causing long-term corticosterone production by adrenals. The latter leads to lipolysis in adipose tissue, followed by β-oxidation and ketogenesis in liver, but also to the reprogramming of GR, whereby GR limits its anti-inflammatory functions. These genome-wide RNAseq and ChIPSeq data, accompanied with studies using GR inhibitor, GR mutant mice and adrenalectomized animals suggest that hypoxia leads to increased sensitivity for acute inflammation and lack of protection by dexamethasone, due to the chronic HPA axis stimulation. Our data unfold new physiological pathways, that may have consequences for patients suffering from GC resistance or living at high altitudes.

overall_design: A total of  conditions were subjected to RNA-seq: Normoxia and hypoxia, each was sequenced with 4 biological replicates.

first: Tineke

last: Vanderhaeghen

first: Deepika

last: Watts

first: Ville

last: Paakinaho

first: Lise

last: Van Wyngene

first: Kelly

last: Van Looveren

first: Jolien

last: Vandewalle

first: Charlotte

last: Wallaeys

first: Louise

last: Nuyttens

first: Melanie

last: Eggermont

first: Sylviane

last: Dewaele

first: Joke

last: Vanden Berghe

first: Joey

last: De Backer

first: Laura

last: Dirkx

first: Sylvia

last: Dewilde

first: Guy

last: Caljon

first: Bart

last: Ghesquière

first: Ben

last: Wielockx

first: Jorma

last: Palvimo

first: Rudi

last: Beyaert

first: Claude

last: Libert


title: Neuronal conversion of human glioblastoma cells by neural transcription factors

city: University Park

first: Gong

last: Chen

state: Pennsylvania

address: Life Science bldg

department: Biology

summary: Purpose: To test the neuronal conversion and other effects induced by neural transcription factor Neurog2 or Ascl1 in human glioblastoma cells  Methods: Retroviral expression of Ascl1, Neurog2 or control GFP in cultured human U251 cells at 6 DPI

overall_design: mRNA profiles of retroviral expression of Ascl1, Neurog2 or control GFP in cultured human U251 cells at 6 DPI

first: Xin

last: Wang


title: The role of chemerin in clear cell renal cell carcinoma

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: The most common subset of renal carcinoma, clear cell renal cell carcinoma (ccRCC), is characterized by accentuated accumulation of neutral lipids in lipid droplets and adipogenic trans-differentiation. Because obesity is a major risk factor in the development of ccRCC, we investigated the role of the adipokines in driving lipid metabolism and tumorigenesis in ccRCC. Through in silico screening, we identified the adipokine chemerin as candidate pro-oncogenic factor that is overexpressed in tumors and prognostic for patient outcome. Both ccRCC patient tumor tissues and serum exhibit elevated chemerin levels as compared to normal controls in an obesity-dependent manner. Attenuation of chemerin by several approaches in ccRCC cells led to significant impairments of tumor growth in both in vitro and in vivo models. A multi-omic approach revealed that chemerin suppresses fatty acid oxidation and maintains fatty acid levels which feed into transcriptional activation of hypoxia-inducible factor 2 (HIF2) expression. Suppression of chemerin therefore induced excess fatty acid oxidation and led to ferroptosis. CoQ and mitochondrial complex IV, derived mainly from lipid, were affected after chemerin inhibition, contributing to mitochondrial dysfunction and lipid reactive oxygen species production. Monoclonal antibody targeting chemerin led to reduced lipid storage, increased cell death, and diminished tumor growth, strengthening the translational potential of chemerin inhibition. Collectively, the results suggest that obesity and tumor cells contribute to ccRCC through the expression of chemerin, which is indispensable in ccRCC biology.

overall_design: mRNA profiling in experimental model of ccRCC 786-O cells. RARRES2 gene is deleted using lentiviral shRNA.

first: Scott

middle: M

last: Welford

first: Sze

last: Tan


title: Reprogramming of glucocorticoid receptor function by hypoxia: RNA-seq after 24h.

first: Steven

last: Timmermans

overall_design: A total of 4 conditions were subjected to RNA-seq: Normoxia+PBS, Hypoxia+PBS, Normoxia+DEX and Hypoxia+DEX. Each of the 4 condictions has 3 biological replicates.

first: Tineke

last: Vanderhaeghen

first: Deepika

last: Watts

first: Ville

last: Paakinaho

first: Lise

last: Van Wyngene

first: Kelly

last: Van Looveren

first: Jolien

last: Vandewalle

first: Charlotte

last: Wallaeys

first: Louise

last: Nuyttens

first: Melanie

last: Eggermont

last: Berghe


title: Gene family expansions and transcriptome signatures uncover adaptations to wood decay in basidiomycetes fungi from the order Polyporales [Irpex lacteus]

city: Marseille

first: Marie-Noëlle

last: Rosso

address: 163 avenue de Luminy

department: Biodiversity and Biotechnology of Fungi - BBF

country: France

institute: INRAE - Aix Marseille University

summary: Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. The transcriptomic trends of selected Polyporales species from the core polyporoid and phlebioid clades during degradation of diverse lignocellulosic substrates led to the discovery of conserved gene sets regulated for plant cell wall degradation. Our results unveil some of the mechanisms underlying Polyporales diversification and pinpoint to yet overlooked proteins that could contribute to the ability of Polyporales to degrade recalcitrant plant cell wall polymers.

overall_design: Examination of mRNA levels in Irpex lacteus CCBAS Fr. 238 617/93  after 3 days growth on maltose, cellulose, wheat straw, ground aspen or ground pine.

first: Igor

last: Grigoriev

first: Anna

last: Lipzen

first: María

last: Martínez

first: Laura

last: de Eugenio


title: Striatal transcriptome changes linked to drug-induced repetitive behaviors

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Disruptive or excessive repetitive motor patterns (stereotypies) are cardinal symptoms in numerous neuropsychiatric disorders. Stereotypies are also evoked by psychomotor stimulants such as amphetamine. The acquisition of motor sequences are paralleled by changes in activity patterns in the striatum, and stereotypies have been linked to abnormal plasticity in these reinforcement-related circuits. Here, we designed experiments in mice to identify transcriptomic changes that underlie striatal plasticity occurring alongside the development of drug-induced stereotypic behavior. We identified three schedules of amphetamine treatment inducing different degrees of stereotypy and used bulk RNAseq to compare striatal gene expression changes among groups of mice treated with the different drug-dose schedules and vehicle-treated, cage-mate controls. Mice were identified as naive, sensitized, or tolerant to drug-induced stereotypy. All drug-treated groups exhibited expression changes in genes that encode members of the extracellular signal-regulated kinase (ERK) cascades known to regulate psychomotor stimulant responses. In the sensitized group with the most prolonged stereotypy, we found dysregulation of 20 genes that were not changed in other groups. Gene set enrichment analysis indicated highly significant overlap with genes regulated by neuregulin 1 (Nrg1). Nrg1 is known to be a schizophrenia and autism susceptibility gene that encodes a ligand for Erb-B receptors, which are involved in neuronal migration, myelination and cell survival, including that of dopamine-containing neurons. Stimulant abuse is a risk factor for schizophrenia onset, and these two disorders share behavioral stereotypy phenotypes. Our results raise the possibility that drug-induced sensitization of the Nrg1 signaling pathway might underlie these links.

overall_design: Striatum of both hemispheres from eighteen sibling mice were compared with 3 mice in each of 6 treatment groups: days 1, 7 and 21 with amphetamine or vehicle treatment.

first: Jill

middle: R

last: Crittenden

first: Theresa

last: Gipson

first: Anne

middle: C

last: Smith

first: Hilary

last: Bowden

first: Ferah

last: Yildrime

first: Kyle

last: Fischer

first: Michael

last: Yima

first: David

last: Housman

first: Ann

last: Graybiel


title: CEBPG promotes esophageal squamous cell carcinoma progression by enhancing PI3K-AKT signaling

city: Guangzhou

first: Yongsheng

last: Huang

address: 107 Yan Jiang West Road

institute: Sun Yat-Sen University

summary: CCAAT enhancer binding proteins (CEBPs) have critical roles in the physiological and pathological processes. However, the characteristics and contributions of CEBPs in esophageal squamous cell carcinoma (ESCC) is unknown. Here, we showed that most of CEBPs (including CEBPA, CEBPB, CEBPE, CEBPG, CEBPZ) were upregulated and amplified in ESCC. Of note, high CEBPG expression is a prognostic factor for the poor survival of patients with ESCC. Moreover, the ESCC specific transcription factor TP63 activates the expression of CEBPG by directly binding to its distal enhancer. Functionally, CEBPG significantly enhances the proliferation and migration of ESCC cells in vitro and in vivo. Mechanistically, CEBPG enhances the PI3K-AKT signaling pathways through directly binding to distal enhancer or/and promoter of downstream target genes, such as CCND1, MYC and CDK2 etc. These findings provide important characteristics and contributions insights into CEBPs dysregulation in ESCC and elucidate a crucial role for CEBPG in the progression of ESCC, which highlights its potential therapeutic target for patients.

overall_design: Retinal mRNA profiles of KYSE150 cells (before and after knockdown CEBPG)  were generated by  deep sequencing

first: Dong

last: Yin


title: Gene family expansions and transcriptome signatures uncover adaptations to wood decay in basidiomycetes fungi from the order Polyporales [Leiotrametes sp.]

first: Marie-Noëlle

last: Rosso

overall_design: Examination of mRNA levels in Leiotrametes sp. BRFM1775  after 3 days growth on maltose, cellulose, wheat straw, ground aspen or ground pine.

first: Delphine

last: Chaduli


title: PD biomarkers for IL-22Fc

city: South San Francisco

first: Kevin

state: California

address: 1 DNA Way

department: Bioinformatics

institute: Genentech

summary:
The goal is to identify an IL-22Fc specific gene signature in human intestinal epithelial cells in order to support PD biomarkers for IL-22Fc. We have identified IL-22Fc specific activity in HT-29 cells as secreted acute phase proteins only in the presence of IL-1β. Therefore, HT-29 cells (from gCell) will be cultured with IL-22, IL-1β, IL-6 (as a pSTAT3 activation control) as well as IL-22 + IL-1β and IL-6 + IL-1β.

The "SAMID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0027983

Keywords: Expression profiling by array

overall_design: Culture HT-29 cells for 5 days in 24 wells plates. Treat cells with cytokine(s) for 24 hours at 37?C. Six groups inluce 1) Media, 2)IL-22Fc, 3)IL-6, 4)IL-1β, 5)IL-22Fc+IL-1β, 6)IL-6+IL-1β. Combine triplicate wells per sample and extract total RNA from whole blood using RNeasy kit with on column DNase treatment. Three biological replicates will be performed, each to be run on a separate chip. 1.5ug RNA at a concentration of >100ng/ml will be submitted for each sample.Culture HT-29 cells for 5 days in 24 wells plates. Treat cells with cytokine(s) for 24 hours at 37?C. Six groups inluce 1) Media, 2)IL-22Fc, 3)IL-6, 4)IL-1β, 5)IL-22Fc+IL-1β, 6)IL-6+IL-1β. Combine triplicate wells per sample and extract total RNA from whole blood using RNeasy kit with on column DNase treatment. Three biological replicates will be performed, each to be run on a separate chip. 1.5ug RNA at a concentration of >100ng/ml will be submitted for each sample.

first: Julie

last: Rae

first: Jason

last: Hsieh


title: The RNA binding protein IGF2BP3 is required MLL-AF4 mediated leukemogenesis

city: Los Angeles

first: Dinesh

last: Rao

address: 650 Charles E Young Dr S

department: Pathology & Lab Medicine

institute: UCLA

summary: In our study, we found that MLL-AF4 transcriptionally induces IGF2BP3 and is required for MLL-Af4 mediated leukemogenesis. Deletion of murine Igf2bp3 significantly increased the survival of mice with MLL-Af4 driven leukemia and greatly attenuated disease. Furthermore, Igf2bp3 was necessary for the development of and the self-renewal capacity of MLL-Af4 leukemic initiating cells. eCLIP and transcriptome analysis of MLL-Af4 transformed stem and progenitor cells and primary cells from MLL-Af4 leukemic mice revealed an IGF2BP3-regulated post-transcriptional operon governing tumor cell survival and proliferation. Critical mRNA targets include the Hoxa locus and numerous genes within the Ras signaling pathway. Together, our findings show that IGF2BP3 is an essential positive regulator of MLL-AF4 mediated leukemogenesis and is a potential therapeutic target in this disease.

overall_design: eCLIP and transcriptome analysis of MLL-Af4 transformed HSPCs and primary cells from MLL-Af4 leukemic mice

first: Tiffany

last: Tran

first: Julia

last: Philipp

first: Jeremy

last: Sanford

middle: S


title: Gene family expansions and transcriptome signatures uncover adaptations to wood decay in basidiomycetes fungi from the order Polyporales [Trametes ljubarskyi]

overall_design: Examination of mRNA levels in Trametes ljubarskyi BRFM1659 after 3 days growth on maltose, cellulose, wheat straw, ground aspen or ground pine.

first: Igor

last: Grigoriev

first: Anna

last: Lipzen


title: Effects of HIF2α in renal cancer metastasis and sensitivity to repurposed drugs

city: Oxford

first: Adrian

middle: L

last: Harris

address: John Radcliffe Hospital

department: Department of Medical Oncology

country: United Kingdom

institute: University of Oxford

summary: Background: in clear cell renal cell carcinoma (ccRCC), 80% of cases have biallelic inactivation of VHL gene, leading to constitutive activation of both HIF1α and HIF2α. As HIF2α is the driver of the disease promoting tumour growth and metastasis, drugs targeting HIF2α have been developed. However, resistance is common, therefore new therapies are needed. Methods: we generated the 786-0 HIF2α knockout (KO) cell line and assessed the HIF2α antagonist PT2385 in several steps of tumour development. RNA sequencing was performed to identify genes differentially expressed between them and a drug screening was used to identify drugs with differential effects on HIF2α-expressing and KO cells. Results: HIF2α KO promoted cell migration, reduced proliferation and clonogenicity, as well as metastasis, whereas PT2385 treatment only inhibited tumour cell invasion. There was a large set of co-ordinately regulated genes, but HIF2α KO cells also had up-regulation of genes related to EMT and downregulation of genes involving cell migration and extracellular matrix. The HIF2α KO increased sensitivity to statins, while PT2385 had no effect. Conclusions: this study shows new pathways that could be targeted combined with PT2385 to enhance its therapeutic effects and delay resistance.

overall_design: Sequencing of RNA extracted from 786-0 parental (WT), 786-0 HIF2a KO and 786-0 WT cells treated with 10uM PT2385 under normoxia conditions. 3 replicates per sample. Total of 9 samples.

first: Esther

last: Arnaiz

first: Ana

last: Miar

last: Bridges

first: Naveen

last: Prasad

first: Stephanie

last: Hatch

first: Charles

last: Lawrie


title: Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia

city: Linköping

first: Shumaila

last: Sayyab

address: Campus US, Building 420, Entrance 68

department: Biomedical and Clinical Sciences (BKV)

institute: Linköping University

summary: Despite high survival rates in pediatric acute lymphoblastic leukemia (ALL), relapse remains a leading cause of cancer-related death in children. Many patients suffer from adverse drug effects during treatment and other complications later in life, and would benefit from improved relapse prediction at diagnosis. We performed whole genome sequencing of samples collected at diagnosis, relapse(s) and remission from 29 Nordic patients with pediatric ALL. Somatic mutations were called using individually matched remission samples as controls, and allelic expression of the mutations in the ALL cells was assessed using RNA-sequencing. These analyses identified 29 previously known ALL driver genes, of which nine genes carried recurrent protein-coding mutations in our sample set, and 20 mutated driver genes occurred in individual samples. We detected putative non-coding mutations in regulatory regions of seven additional genes that have not been described previously in ALL. We observed an increased burden of somatic mutations at relapse. Cluster analysis of hundreds of somatic mutations per sample revealed three distinct evolutionary trajectories during ALL progression. In an “ancestral clone trajectory”, the major cell clone at relapse originated from a founder clone that was not detectable at diagnosis. In a “rising diagnostic clone trajectory”, a minor cell clone at diagnosis expanded to form the major cell clone at relapse. In a “persistent diagnostic clone trajectory”, the major cell clone at diagnosis persisted during treatment until relapse. The evolutionary trajectories provide insight into the mutational mechanisms leading relapse in ALL and could offer biomarkers for improved risk prediction in individual patients.

overall_design:
RNA-sequencing (RNA-seq) libraries were prepared from RNA available from ALL patients at diagnosis (n=22), at first relapse (n=25), at second relapse (n=7) and control B-cells (CD19+) and T-cells (CD3+) from five healthy Swedish individuals as described in Marincevic-Zuniga et al. Thirty million sequence read pairs (paired-end, 65bp) per sample were generated per library on a HiSeq2500 instrument,

*** Raw data not provided due to patient privacy concerns ***

first: Ann-Christine

last: Syvänen


title: DPP-4 inhibitor MK-626 improves vascular endothelial function by modulating lncRNA and mRNA expression profiles in Ang II-induced hypertensive mouse aortae.

city: BeiJing

last: Tan

address: No. 38 Xue Yuan Road

institute: Peking University Health Science Center

summary: To investigated the therapeutic mechanism underlying the  MK-626 improves vascular endothelial functionin hypertension,  we performed bioinformatics analyses on the expression profiles of  long noncoding RNAs (lncRNAs) and message RNAs (mRNAs) and in the aortae from Ang Ⅱ-induced hypertensive mice with or without MK-626 treatment.

overall_design:
The animals were divided to the following three groups (3 mice per group): (i) C57BL/6J as Vehicle group; (ii) Ang II infused C57BL/6J without oral MK-626 treatment (Ang II); (iii) Ang II infused C57BL/6J (1 mg/kg/d) with oral MK-626 treatment (3 mg/kg/d) (Ang II+ MK-626).
The microarray data of the first two groups also belong to GSE159725 study.

first: Yi

last: Zhang


title: Identification of three enzymes of the vanillin and vanillic acid metabolic pathway in the filamentous fungi Aspergillus niger

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

summary: The aim of this study was to find candidate genes in A. niger involved in the vanillic acid metabolic pathway.

overall_design: Transcriptome data on aromatic compounds was used to find candidate genes encoding aromatic metabolic enzymes

first: Ronnie

middle: J

last: Lubbers

first: Mao

last: Peng

middle: P


title: Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum Flower Transcriptomes

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

summary: RNA sequencing  in tomato for detect mRNA expression of Solanum lycopersicum flower.The two cultivars (monomaker, raceme) had three different flowering stages (budlet, Flower bud, Full bloom) for transcriptome sequencing

overall_design: This study aimed to investigates lots of different expressed genes. All tomato  flower tissues of two cultivars (monomaker, Compound raceme) were collected and used to RNA sequencing.

first: Yahui

last: Yang


title: Gene family expansions and transcriptome signatures uncover adaptations to wood decay in basidiomycetes fungi from the order Polyporales [Trametes elegans]

first: Marie-Noëlle

last: Rosso

last: Grigoriev

last: Lipzen

first: Delphine

last: Chaduli


title: Transcriptomic analysis of endothelial progenitor cells (EPCs) isolated from mice exposed to concentrated air pollution particles (CAPS) [miRNA-seq]

city: Louisville

first: Timothy

last: O'Toole

state: KY

address: 302E. Muhammad Ali Blvd

institute: University of Louisville

summary: Mice were exposed to filtered air or CAPs for 30 days and then bone marrow-derived EPCs isolated and cultured for 12 days. RNAs isolated from these mice were used for RNA seq analysis.

overall_design: We report change in miRNA species between the two exposure conditions.

first: Xiaohong

last: Li


title: Transcriptomic analysis of endothelial progenitor cells (EPCs) isolated from mice exposed to concentrated air pollution particles

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: N6-methyladenosine RNA methylome analyses in human prostate cell lines.

city: San Antonio

first: Kexin

last: Xu

state: Texas

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

summary: To identify N6-methyladenosine RNA methylome in human prostate cell lines, MeRIP-seq of RWPE-1 and LNCaP were performed.

overall_design: N6-methyladenosine RNA methylome profiling by high throughput sequencing (MeRIP-seq)

first: Zhao

first: Jihoon

last: Lee


title: RNA transcriptome analyses in shcontrol, shMETTL3, shMETTL3-resistant METTL3 wildtype and catalytically dead mutant LNCaP cells.

summary: To investigate the role of METTL3-mediated m6A modification, we performed transcriptome profiling by high throughput sequencing.

overall_design: Total RNA etraction followed by high throughput sequencing (RNA-seq) in shControl, shMETTL3, shMETTL3-resistant METTL3 wildtype and mutant (catalytically dead) stable LNCaP cell lines


title: Stomach-specific c-Myc overexpression drives intestinal-type gastric cancer in mice via AKT/mTOR signaling

city: Shanghai

first: Jing

last: Liu

address: Huashan Road 1954

institute: Shanghai Jiao Tong University

summary: Gastric cancer (GC) is one of the most common malignant cancers in the world. c-Myc, a well-known oncogene, is commonly amplified in many cancers, including gastric cancer. However, it is still not completely understood how c-Myc functions in GC. Here, we generated a stomach-specific c-Myc knock-in mouse model to investigate its role in GC. We found that overexpression of c-Myc in Atp4b+ gastric parietal cells could induce intestinal-type gastric cancer in mice. Mechanistically, c-Myc promoted tumorigenesis via the AKT/mTOR pathway. Furthermore, AKT inhibitor (MK-2206) or mTOR inhibitor (Rapamycin) inhibited the proliferation of c-Myc overexpressing gastric cancer cell lines. Thus, our findings highlight that gastric cancer can be induced by c-Myc overexpression through activation of the AKT/mTOR pathway.

overall_design: Gastric mRNA profiles of 12-week old wild type (WT) and Atp4b-cre;MycOE mice were generated by deep sequencing, in triplicate.

first: Li


title: human prostate cell lines


title: Transcriptomic analysis of endothelial progenitor cells (EPCs) isolated from mice exposed to concentrated air pollution particles (CAPS) [mRNA-seq]

overall_design: We report change in mRNA species between the two exposure conditions.


title: ChIP-seq identified transcription factor UvCGBP1-mediated target genes of Ustilaginoidea virens

city: Wuhan

first: Zhou

last: Jian

address: Wuhan China

institute: AJBK

summary: Transcription factor UvCGBP1 (Cutinase G-box binding protein) is a new transcription factor and it specificlly distributed in Ascomycetes.We used ChIP-seq identified more than 2000 target genes, we provide a comprehensive genome-wide binding map of CGBP1 and its regulatory network. Our results  reveal new insights into the mechanism of CGBP1-mediated gene regulation in the plant fungal pathogen.

overall_design: Identification of downstream target genes regulated by the transcription factor UvCGBP1.

first: Xiaoyang

last: Chen

first: Junbin

last: Huang

first: Lu

last: Zheng


title: Integrative Hi-C maps of pancreatic cancer

city: Beijing

first: Bo

last: Ren

address: Shuaifuyuan #1

department: General Surgery

institute: Peking Union Medical College Hospital

summary: Pancreatic cancer's poor prognosis is caused by distal metastasis, which is associated with epigenomic changes. However, the roles of 3D epigenome in pancreatic cancer biology, especially its metastasis, remain unclear. Here we compare the 3D epigenomic and transcriptomic features among cells derived from pancreatic epithelial, primary and metastatic pancreatic cancer by integrated analysis of in situ Hi-C, ChIP-seq, ATAC-seq, and RNA-seq data. We found A/B compartments, topologically associated domains (TADs), chromatin loops changed significantly in metastatic pancreatic cancer cells, which is associated with epigenetic state alterations. Moreover, we identified upregulated genes, which are located in switched compartments, common TADs with epigenetic state changing, specific TAD boundaries, and metastasis-specific enhancer-promoter loops, are related to cancer metastasis. We also find that the transcription factors mediated specific enhancer-promoter loops formation are also associated with metastasis. Taken together, these results provide a 3D epigenomic map of pancreatic cancer metastasis, which expands our knowledge of the epigenetic mechanism of pancreatic cancer metastasis and enables a better understanding of pancreatic cancer pathobiology.

overall_design: We used in situ Hi-C to identify chromatin interactions, ChIP-seq to identify chromatin states and CTCF binding sites, ATAC-seq to evaluate chromomsome accessibility, and RNA-seq to profile transcriptomes in normal (HPNE) and pancreatic cancer cells derived from primary sites (PANC-1) and liver metastasis (Capan-1).

first: Jinshou

first: Gang

first: Huanyu

first: Yuan

first: Xuning

last: Fan

first: Lei

last: You

first: Taiping

last: Zhang

first: Yupei

last: Zhao